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<title>Stromal Signal Calculator Process</title>
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		<a href="selection.jsp">Start Stromal Signal Calculator</a>
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					<h1 style="text-align: center;">Data Preparation</h1>
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								Process all selected samples together using chosen method: <a
									href="http://media.affymetrix.com/support/technical/technotes/plier_technote.pdf"
									title="Probe Logarithmic Intensity Error (PLIER). This option implements Affymetrix's PLIER algorithm.">PLIER</a>,
								<a
									href="http://media.affymetrix.com/support/technical/whitepapers/sadd_whitepaper.pdf"
									title="This option computes Bioconductor's implementation of Affymetrix's MAS 5.0 expression measure as described in Statistical Algorithms Description Document by Affymetrix.">MAS5</a>,
								or <a
									href="http://biostatistics.oxfordjournals.org/content/4/2/249.long"
									title="This option computes the RMA (Robust Multichip Average) expression measure.">RMA.</a>
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							<h3>Quantile normalize processed samples. This results in
								all of the samples having the same expression distribution.</h3>
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						P<sub>Lymphoid</sub> Estimations (per group*)
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							<h3>Calculate average whole tissue signal and average
								lymphoid signal for each probe set.</h3>
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						<li><h3>Calculate [average whole tissue signal]/[average
								lymphoid signal] ratio for each probe set.</h3></li>
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					<h3>a. Rank Ordered Ratio Estimates</h3>
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							<h3>Sort ratios smallest to largest.</h3>
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							<h3>Remove ratio values greater than 2.</h3>
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								Determine cubic polynomial curve estimation ( f(x) = ax<sup>3</sup>
								+ bx<sup>2</sup> + cx + d ) of rank ordered ratio.
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								Determine x<sub>inflection</sub>. x<sub>inflection</sub> is
								where f"(x)=0
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								<a href="http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2807413/">Perpendicular
									estimate</a> is y<sub>inflection</sub> = f(x<sub>inflection</sub>)
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								<a href="http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2807413/">Tangent
									estimate</a> is the y-intercept of tangent line to inflection point
								= y<sub>inflection</sub> - f'(x<sub>inflection</sub>) * x<sub>inflection</sub>
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						b. <a href="http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2807413/">Lymphoid-specific
							gene estimate</a> is the average of the ratios of a manually curated
						list of genes known to be expressed by lymphoid cells but not by
						other cell types (Rag1, CD4, Lck, etc);

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					<h1 style="text-align: center;">Stromal Signal Calculation
						(per group*)</h1>
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								[calculated stromal signal] =( [average whole tissue signal] -
								[P<sub>Lymphoid</sub>] * [average lymphoid signal] ) / ( 1 - [P<sub>Lymphoid</sub>]
								)
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							<h3>Quantile normalize calculated stromal expression to the
								selected samples' expression distribution.</h3>
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			<td>*Group refers to time point and tissue type of the selected samples.
				(ie. Five weeks old cortex, Day 12 after castration medulla)</td>
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